Selenium and Te are two important critical metals, which are often produced as by-products in Au-Cu deposits related to magmatic–hydrothermal systems, such as porphyry and skarn deposits. The Jilongshan Au-Cu deposit is a typical skarn deposit located in the middle and lower parts of the Yangtze River metallogenic belt. Previous studies show that it has valuable Se and Te resources, but their occurrence, particularly the relationship between the texture and composition of pyrite, and the enrichment mechanism of Se, Te, and Au remain unclear. Here, the textures and the major and trace elements of the Jilongshan pyrites were studied by using an optical microscope, EMPA, and LA-ICP-MS to reveal the occurrence of Se, Te, and Au in pyrite, as well as their genetic links with the pyrite mineralogical signature. The results show that there are three types of ores in the Jilongshan deposit, including granite porphyry-hosted, skarn-hosted, and carbonate-hosted ores. All of these ores contain major amounts of pyrite, which can be divided into four different generations. The first generation of pyrite (Py1) belongs to sedimentary genesis with a typical framboid texture and its Co/ Ni ratios are less than 1, whereas Py2, Py3, and Py4 belong to hydrothermal genesis and their Co/ Ni ratios are between 1.0 and 30.2. Selenium concentrations in Py2 and Py3 are relatively high (median, 138 ppm and 344 ppm, respectively), which are mainly present as isomorphism and a small amount as selenite in pyrite. Compared with granite porphyry-hosted and skarn-hosted ores, pyrite from carbonate-hosted ores has the highest Se concentrations. The latest generation of pyrite (Py4) contains the highest concentrations of Te (average, 140 ppm) and Au (average, 12 ppm) among the hydrothermal pyrites. Therefore, the precipitation of Se mainly occurs in pyrite during the early high-temperature stage, whereas higher concentrations of Te and Au are mainly enriched in pyrite during the late stage with low temperatures.